1
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Chamorro A, Rossetti M, Bagheri N, Porchetta A. Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:71-106. [PMID: 38273204 DOI: 10.1007/10_2023_235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.
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Affiliation(s)
| | - Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
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2
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Chang J, Zou D, Ren H, Liu X, Li M, Si Z, Han C, Liu Z, Lu S, Hu P. An ultrasensitive and long-lasting chemiluminescence immunoassay for IP-10 detection based on a 4-bromophenol-reinforced bienzymatic system. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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3
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Biodetection Techniques for Quantification of Chemokines. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10080294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chemokines are a class of cytokine whose special properties, together with their involvement and relevant role in various diseases, make them a restricted group of biomarkers suitable for diagnosis and monitoring. Despite their importance, biodetection techniques dedicated to the selective determination of one or more chemokines are very scarce. For some years now, the critical diagnosis of inflammatory diseases by detecting both cytokine and chemokine biomarkers, has had a strong impact on the development of multiple detection platforms. However, it would be desirable to implement methodologies with a higher degree of selectivity for chemokines, in order to provide more precise information. In addition, better development of biosensor technology applied to this specific field would make it possible to address the main challenges of detection methods for several diseases with a high incidence in the population, avoiding high costs and low sensitivity. Taking this into account, this review aims to present the state of the art of chemokine biodetection techniques and emphasize the role of these systems in the prevention, monitoring and treatment of various diseases associated with chemokines as a starting point for future developments that are also analyzed throughout the article.
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4
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Nguyen ABN, Maldonado M, Poch D, Sodia T, Smith A, Rowland TJ, Bonham AJ. Electrochemical DNA Biosensor That Detects Early Celiac Disease Autoantibodies. SENSORS 2021; 21:s21082671. [PMID: 33920183 PMCID: PMC8070315 DOI: 10.3390/s21082671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/26/2022]
Abstract
Although it is estimated that more than one million Americans have celiac disease (CD), it remains challenging to diagnose. CD, an autoimmune and inflammatory response following the ingestion of gluten-containing foods, has symptoms overlapping with other diseases and requires invasive diagnostics. The gold standard for CD diagnosis involves serologic blood tests followed by invasive confirmatory biopsies. Here, we propose a less invasive method using an electrochemical DNA (E-DNA) biosensor for CD-specific autoantibodies (AABs) circulating in blood. In our approach, CD-specific AABs bind a synthetic neoepitope, causing a conformational change in the biosensor, as well as a change in the environment of an attached redox reporter, producing a measurable current reduction. We assessed the biosensor’s ability to detect CD-specific patient-derived AABs in physiological buffer as well as buffer supplemented with bovine serum. Our biosensor was able to detect AABs in a dose-dependent manner; increased signal change correlated with increased AAB concentration with an apparent dissociation constant of 0.09 ± 0.03 units/mL of AABs. Furthermore, we found our biosensor to be target-specific, with minimal off-target binding of multiple unrelated biomarkers. Future efforts aimed at increasing sensitivity in complex media may build upon the biosensor design presented here to further improve CD AAB detection and CD diagnostic tools.
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Affiliation(s)
- Anna B. N. Nguyen
- Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106, USA;
| | - Marcos Maldonado
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA; (M.M.); (D.P.); (T.S.); (A.S.)
| | - Dylan Poch
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA; (M.M.); (D.P.); (T.S.); (A.S.)
| | - Tyler Sodia
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA; (M.M.); (D.P.); (T.S.); (A.S.)
| | - Andrew Smith
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA; (M.M.); (D.P.); (T.S.); (A.S.)
| | - Teisha J. Rowland
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA;
| | - Andrew J. Bonham
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA; (M.M.); (D.P.); (T.S.); (A.S.)
- Correspondence:
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5
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Traynor SM, Wang GA, Pandey R, Li F, Soleymani L. Dynamic Bio‐Barcode Assay Enables Electrochemical Detection of a Cancer Biomarker in Undiluted Human Plasma: A Sample‐In‐Answer‐Out Approach. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sarah M. Traynor
- Department of Biomedical Engineering McMaster University 1280 Main St. W. Hamilton ON Canada
| | - Guan A. Wang
- Department of Chemistry Brock University 1812 Sir Isaac Brock Way St. Catharines ON Canada
| | - Richa Pandey
- Department of Engineering Physics McMaster University 1280 Main St. W. Hamilton ON Canada
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education College of Chemistry Brock University Canada
| | - Leyla Soleymani
- Department of Biomedical Engineering McMaster University 1280 Main St. W. Hamilton ON Canada
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6
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Traynor SM, Wang GA, Pandey R, Li F, Soleymani L. Dynamic Bio‐Barcode Assay Enables Electrochemical Detection of a Cancer Biomarker in Undiluted Human Plasma: A Sample‐In‐Answer‐Out Approach. Angew Chem Int Ed Engl 2020; 59:22617-22622. [DOI: 10.1002/anie.202009664] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Sarah M. Traynor
- Department of Biomedical Engineering McMaster University 1280 Main St. W. Hamilton ON Canada
| | - Guan A. Wang
- Department of Chemistry Brock University 1812 Sir Isaac Brock Way St. Catharines ON Canada
| | - Richa Pandey
- Department of Engineering Physics McMaster University 1280 Main St. W. Hamilton ON Canada
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education College of Chemistry Brock University Canada
| | - Leyla Soleymani
- Department of Biomedical Engineering McMaster University 1280 Main St. W. Hamilton ON Canada
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7
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Holtan MD, Somasundaram S, Khuda N, Easley CJ. Nonfaradaic Current Suppression in DNA-Based Electrochemical Assays with a Differential Potentiostat. Anal Chem 2019; 91:15833-15839. [PMID: 31718147 DOI: 10.1021/acs.analchem.9b04149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
One of the key factors limiting sensitivity in many electrochemical assays is the nonfaradaic or capacitive current. This is particularly true in modern assay systems based on DNA monolayers at gold electrode surfaces, which have shown great promise for bioanalysis in complex milieu such as whole blood or serum. While various changes in analytical parameters, redox reporter molecules, DNA structures, probe coverage, and electrode surface area have been shown useful, background reduction by hardware subtraction has not yet been explored for these assays. Here, we introduce new electrochemistry hardware that considerably suppresses nonfaradaic currents through real-time analog subtraction during current-to-voltage conversion in the potentiostat. This differential potentiostat (DiffStat) configuration is shown to suppress or remove capacitance currents in chronoamperometry, cyclic voltammetry, and square-wave voltammetry measurements applied to nucleic acid hybridization assays at the electrode surface. The DiffStat makes larger electrodes and higher sensitivity settings accessible to the user, providing order-of-magnitude improvements in sensitivity, and it also significantly simplifies data processing to extract faradaic currents in square-wave voltammetry (SWV). Because two working electrodes are used for differential measurements, unique arrangements are introduced such as converting signal-OFF assays to signal-ON assays or background drift correction in 50% human serum. Overall, this new potentiostat design should be helpful not only in improving the sensitivity of most electrochemical assays, but it should also better support adaptation of assays to the point-of-care by circumventing complex data processing.
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Affiliation(s)
- Mark D Holtan
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Subramaniam Somasundaram
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Niamat Khuda
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Christopher J Easley
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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8
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Ogden NE, Kurnik M, Parolo C, Plaxco KW. An electrochemical scaffold sensor for rapid syphilis diagnosis. Analyst 2019; 144:5277-5283. [PMID: 31369000 PMCID: PMC6886667 DOI: 10.1039/c9an00455f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The faster a disease can be diagnosed, the sooner effective treatment can be initiated, motivating a drive to replace standard laboratory techniques with point-of-care technologies that return answers in minutes rather than hours. Thus motivated, we describe the development of an E-DNA scaffold sensor for the rapid and convenient measurement of antibodies diagnostic of syphilis. To achieve this (and in contrast to previous sensors of this class, which relied on single, linear epitopes for detection), we utilized a near full-length antigen as the sensor's recognition element, allowing us to simultaneously display multiple epitopes. The resultant sensor is able to detect antibodies against Treponema pallidum pallidum, the causative agent of syphilis, at clinically relevant concentrations in samples in less than 10 min. Preliminary results obtained using sero-positive and sero-negative human samples suggest the clinical sensitivity and specificity of the approach compare well to current gold-standard tests, while being simple and rapid enough to deploy at the point of care.
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Affiliation(s)
- Nathan E Ogden
- Department of Material Science and Engineering, University of California, Santa Barbara, CA 93106, USA
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9
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Somasundaram S, Easley CJ. A Nucleic Acid Nanostructure Built through On-Electrode Ligation for Electrochemical Detection of a Broad Range of Analytes. J Am Chem Soc 2019; 141:11721-11726. [PMID: 31257869 DOI: 10.1021/jacs.9b06229] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For an assay to be most effective in point-of-care clinical analysis, it needs to be economical, simple, generalizable, and free from tedious workflows. While electrochemistry-based DNA sensors reduce instrumental costs and eliminate complicated procedures, there remains a need to address probe costs and generalizability, as numerous probes with multiple conjugations are needed to quantify a wide range of biomarkers. In this work, we have opened a route to circumvent complicated multiconjugation schemes using enzyme-catalyzed probe construction directly on the surface of the electrode. With this, we have created a versatile DNA nanostructure probe and validated its effectiveness by quantification of proteins (streptavidin, anti-digoxigenin, anti-tacrolimus) and small molecules (biotin, digoxigenin, tacrolimus) using the same platform. Tacrolimus, a widely prescribed immunosuppressant drug for organ transplant patients, was directly quantified with electrochemistry for the first time, with the assay range matching the therapeutic index range. Finally, the stability and sensitivity of the probe was confirmed in a background of minimally diluted human serum.
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Affiliation(s)
- Subramaniam Somasundaram
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Christopher J Easley
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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10
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Hu Z, Suo Z, Liu W, Zhao B, Xing F, Zhang Y, Feng L. DNA conformational polymorphism for biosensing applications. Biosens Bioelectron 2019; 131:237-249. [PMID: 30849723 DOI: 10.1016/j.bios.2019.02.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 12/12/2022]
Abstract
In this mini review, we will briefly introduce the rapid development of DNA conformational polymorphism in biosensing field, including canonical DNA duplex, triplex, quadruplex, DNA origami, as well as more functionalized DNAs (aptamer, DNAzyme etc.). Various DNA structures are adopted to play important roles in sensor construction, through working as recognition receptor, signal reporter or linking staple for signal motifs, etc. We will mainly summarize their recent developments in DNA-based electrochemical and fluorescent sensors. For the electrochemical sensors, several types will be included, e.g. the amperometric, electrochemical impedance, electrochemiluminescence, as well as field-effect transistor sensors. For the fluorescent sensors, DNA is usually modified with fluorescent molecules or novel nanomaterials as report probes, excepting its core recognition function. Finally, general conclusion and future perspectives will be discussed for further developments.
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Affiliation(s)
- Ziheng Hu
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China
| | - Zhiguang Suo
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China
| | - Wenxia Liu
- Department of Chemistry, College of Science, Shanghai University, 200444 Shanghai, China
| | - Biying Zhao
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China
| | - Feifei Xing
- Department of Chemistry, College of Science, Shanghai University, 200444 Shanghai, China
| | - Yuan Zhang
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China.
| | - Lingyan Feng
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China.
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11
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Kang D, Parolo C, Sun S, Ogden NE, Dahlquist FW, Plaxco KW. Expanding the Scope of Protein-Detecting Electrochemical DNA "Scaffold" Sensors. ACS Sens 2018; 3:1271-1275. [PMID: 29877078 DOI: 10.1021/acssensors.8b00311] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to measure the levels of diagnostically relevant proteins, such as antibodies, directly at the point of care could significantly impact healthcare. Thus motivated, we explore here the E-DNA "scaffold" sensing platform, a rapid, convenient, single-step means to this end. These sensors comprise a rigid nucleic acid "scaffold" attached via a flexible linker to an electrode and modified on its distal end with a redox reporter and a protein binding "recognition element". The binding of a targeted protein reduces the efficiency with which the redox reporter approaches the electrode, resulting in an easily measured signal change when the sensor is interrogated voltammetrically. Previously we have demonstrated scaffold sensors employing a range of low molecular weight haptens and linear peptides as their recognition elements. Expanding on this here we have characterized sensors employing much larger recognition elements (up to and including full length proteins) in order to (1) define the range of recognition elements suitable for use in the platform; (2) better characterize the platform's signaling mechanism to aid its design and optimization; and (3) demonstrate the analytical performance of sensors employing full-length proteins as recognition elements. In doing so we have enlarged the range of molecular targets amenable to this rapid and convenient sensing platform.
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12
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Kang D, Sun S, Kurnik M, Morales D, Dahlquist FW, Plaxco KW. New Architecture for Reagentless, Protein-Based Electrochemical Biosensors. J Am Chem Soc 2017; 139:12113-12116. [PMID: 28789522 DOI: 10.1021/jacs.7b05953] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Here we demonstrate a new class of reagentless, single-step sensors for the detection of proteins and peptides that is the electrochemical analog of fluorescence polarization (fluorescence anisotropy), a versatile optical approach widely employed to this same end. Our electrochemical sensors consist of a redox-reporter-modified protein (the "receptor") site-specifically anchored to an electrode via a short, flexible polypeptide linker. Interaction of the receptor with its binding partner alters the efficiency with which the reporter approaches the electrode surface, thus causing a change in redox current upon voltammetric interrogation. As our first proof-of-principle we employed the bacterial chemotaxis protein CheY as our receptor. Interaction with either of CheY's two binding partners, the P2 domain of the chemotaxis kinase, CheA, or the 16-residue "target region" of the flagellar switch protein, FliM, leads to easily measurable changes in output current that trace Langmuir isotherms within error of those seen in solution. Phosphorylation of the electrode-bound CheY decreases its affinity for CheA-P2 and enhances its affinity for FliM in a manner likewise consistent with its behavior in solution. As expected given the proposed sensor signaling mechanism, the magnitude of the binding-induced signal change depends on the placement of the redox reporter on the receptor. Following these preliminary studies with CheY, we also developed and characterized additional sensors aimed at the detection of specific antibodies using the relevant protein antigens as the receptor. These exhibit excellent detection limits for their targets without the use of reagents or wash steps. This novel, protein-based electrochemical sensing architecture provides a new and potentially promising approach to sensors for the single-step measurement of specific proteins and peptides.
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Affiliation(s)
- Di Kang
- Department of Chemistry and Biochemistry, ‡Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Sheng Sun
- Department of Chemistry and Biochemistry, ‡Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Martin Kurnik
- Department of Chemistry and Biochemistry, ‡Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Demosthenes Morales
- Department of Chemistry and Biochemistry, ‡Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, ‡Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, ‡Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
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13
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Li H, Dauphin-Ducharme P, Ortega G, Plaxco KW. Calibration-Free Electrochemical Biosensors Supporting Accurate Molecular Measurements Directly in Undiluted Whole Blood. J Am Chem Soc 2017; 139:11207-11213. [PMID: 28712286 DOI: 10.1021/jacs.7b05412] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The need to calibrate to correct for sensor-to-sensor fabrication variation and sensor drift has proven a significant hurdle in the widespread use of biosensors. To maintain clinically relevant (±20% for this application) accuracy, for example, commercial continuous glucose monitors require recalibration several times a day, decreasing convenience and increasing the chance of user errors. Here, however, we demonstrate a "dual-frequency" approach for achieving the calibration-free operation of electrochemical biosensors that generate an output by using square-wave voltammetry to monitor binding-induced changes in electron transfer kinetics. Specifically, we use the square-wave frequency dependence of their response to produce a ratiometric signal, the ratio of peak currents collected at responsive and non- (or low) responsive square-wave frequencies, which is largely insensitive to drift and sensor-to-sensor fabrication variations. Using electrochemical aptamer-based (E-AB) biosensors as our test bed, we demonstrate the accurate and precise operation of sensors against multiple drugs, achieving accuracy in the measurement of their targets of within better than 20% across dynamic ranges of up to 2 orders of magnitude without the need to calibrate each individual sensor.
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Affiliation(s)
- Hui Li
- Faculty of Materials Science and Chemistry, China University of Geosciences , Wuhan 430074, China.,Department of Chemistry and Biochemistry, University of California Santa Barbara , Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California Santa Barbara , Santa Barbara, California 93106, United States
| | - Philippe Dauphin-Ducharme
- Department of Chemistry and Biochemistry, University of California Santa Barbara , Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California Santa Barbara , Santa Barbara, California 93106, United States
| | - Gabriel Ortega
- Department of Chemistry and Biochemistry, University of California Santa Barbara , Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California Santa Barbara , Santa Barbara, California 93106, United States.,CIC bioGUNE , Bizkaia Technology Park, Building 801 A, 48170 Derio, Spain
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California Santa Barbara , Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California Santa Barbara , Santa Barbara, California 93106, United States
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14
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Zhou W, Mahshid SS, Wang W, Vallée-Bélisle A, Zandstra PW, Sargent EH, Kelley SO. Steric Hindrance Assay for Secreted Factors in Stem Cell Culture. ACS Sens 2017; 2:495-500. [PMID: 28723184 DOI: 10.1021/acssensors.7b00136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ex vivo expansion of hematopoietic stem cells is significantly inhibited by secreted proteins that induce negative feedback loops. The ability to effectively monitor these factors is critical for their real-time regulation and control and, by extension, enhancing stem cell expansion. Here, we describe a novel monitoring strategy for the detection of soluble signaling factors in stem cell cultures using a DNA-based sensing mechanism on a chip-based nanostructured microelectrode platform. We combine DNA hybridization engineering with antibody-capturing chemistry in an amplified steric hindrance hybridization assay. This method enables the quantification of important secreted proteins, showcased by the detection of 10 pg·mL-1 level concentrations of three proteins in stem cell culture samples. This approach is the first universal nonsandwich technique that permits pg·mL-1 level quantification of small proteins in stem cell culture media without signal loss.
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Affiliation(s)
- Wendi Zhou
- Electrical
and Computer Engineering, University of Toronto, Toronto M5S 1A4 Canada
| | - Sahar S. Mahshid
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2 Canada
| | - Weijia Wang
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto M5S 3G9 Canada
| | | | - Peter W. Zandstra
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto M5S 3G9 Canada
| | - Edward H. Sargent
- Electrical
and Computer Engineering, University of Toronto, Toronto M5S 1A4 Canada
| | - Shana O. Kelley
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2 Canada
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto M5S 3G9 Canada
- Department
of Biochemistry, University of Toronto, Toronto M5S 1A8 Canada
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15
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Salimian R, Kékedy-Nagy L, Ferapontova EE. Specific Picomolar Detection of a Breast Cancer Biomarker HER-2/neu
Protein in Serum: Electrocatalytically Amplified Electroanalysis by the Aptamer/PEG-Modified Electrode. ChemElectroChem 2017. [DOI: 10.1002/celc.201700025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Razieh Salimian
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Center for DNA Nanotechnology (CDNA) at iNANO
- Sharif University of Technology; Teheran Iran
| | - László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Center for DNA Nanotechnology (CDNA) at iNANO
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Center for DNA Nanotechnology (CDNA) at iNANO
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16
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Islam F, Haque MH, Yadav S, Islam MN, Gopalan V, Nguyen NT, Lam AK, Shiddiky MJA. An electrochemical method for sensitive and rapid detection of FAM134B protein in colon cancer samples. Sci Rep 2017; 7:133. [PMID: 28273937 PMCID: PMC5428029 DOI: 10.1038/s41598-017-00206-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/14/2017] [Indexed: 12/29/2022] Open
Abstract
Despite the excellent diagnostic applications of the current conventional immunoassay methods such as ELISA, immunostaining and Western blot for FAM134B detection, they are laborious, expensive and required a long turnaround time. Here, we report an electrochemical approach for rapid, sensitive, and specific detection of FAM134B protein in biological (colon cancer cell extracts) and clinical (serum) samples. The approach utilises a differential pulse voltammetry (DPV) in the presence of the [Fe(CN)6]3-/4- redox system to quantify the FAM134B protein in a two-step strategy that involves (i) initial attachment of FAM134B antibody on the surface of extravidin-modified screen-printed carbon electrode, and (ii) subsequent detection of FAM134B protein present in the biological/clinical samples. The assay system was able to detect FAM134B protein at a concentration down to 10 pg μL-1 in phosphate buffered saline (pH 7.4) with a good inter-assay reproducibility (% RSD = <8.64, n = 3). We found excellent sensitivity and specificity for the analysis of FAM134B protein in a panel of colon cancer cell lines and serum samples. Finally, the assay was further validated with ELISA method. We believe that our assay could potentially lead a low-cost alternative to conventional immunological assays for target antigens analysis in point-of-care applications.
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Affiliation(s)
- Farhadul Islam
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Australia
| | - Md Hakimul Haque
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Australia.,School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Sharda Yadav
- School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia.,Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Md Nazmul Islam
- School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia.,Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Alfred K Lam
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Australia.
| | - Muhammad J A Shiddiky
- School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia. .,Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia.
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17
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Boyd-Moss M, Baratchi S, Di Venere M, Khoshmanesh K. Self-contained microfluidic systems: a review. LAB ON A CHIP 2016; 16:3177-92. [PMID: 27425637 DOI: 10.1039/c6lc00712k] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Microfluidic systems enable rapid diagnosis, screening and monitoring of diseases and health conditions using small amounts of biological samples and reagents. Despite these remarkable features, conventional microfluidic systems rely on bulky expensive external equipment, which hinders their utility as powerful analysis tools outside of research laboratories. 'Self-contained' microfluidic systems, which contain all necessary components to facilitate a complete assay, have been developed to address this limitation. In this review, we provide an in-depth overview of self-contained microfluidic systems. We categorise these systems based on their operating mechanisms into three major groups: passive, hand-powered and active. Several examples are provided to discuss the structure, capabilities and shortcomings of each group. In particular, we discuss the self-contained microfluidic systems enabled by active mechanisms, due to their unique capability for running multi-step and highly controllable diagnostic assays. Integration of self-contained microfluidic systems with the image acquisition and processing capabilities of smartphones, especially those equipped with accessory optical components, enables highly sensitive and quantitative assays, which are discussed. Finally, the future trends and possible solutions to expand the versatility of self-contained, stand-alone microfluidic platforms are outlined.
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Affiliation(s)
| | - Sara Baratchi
- School of Health & Biomedical Sciences, RMIT University, Melbourne, Victoria, Australia.
| | - Martina Di Venere
- School of Civil & Industrial Engineering, Sapienza University, Rome, Italy
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18
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Feng L, Lyu Z, Offenhäusser A, Mayer D. Electrochemically triggered aptamer immobilization via click reaction for vascular endothelial growth factor detection. Eng Life Sci 2016. [DOI: 10.1002/elsc.201600068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Lingyan Feng
- Peter Grünberg Institute, PGI-8, Bioelectronics, Research Center Jülich; JARA-Fundamentals of Future Information Technology; Jülich Germany
- Materials Genome Institute; Shanghai University; Shanghai China
| | - Zhaozi Lyu
- Peter Grünberg Institute, PGI-8, Bioelectronics, Research Center Jülich; JARA-Fundamentals of Future Information Technology; Jülich Germany
| | - Andreas Offenhäusser
- Peter Grünberg Institute, PGI-8, Bioelectronics, Research Center Jülich; JARA-Fundamentals of Future Information Technology; Jülich Germany
| | - Dirk Mayer
- Peter Grünberg Institute, PGI-8, Bioelectronics, Research Center Jülich; JARA-Fundamentals of Future Information Technology; Jülich Germany
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19
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Jarczewska M, Kékedy-Nagy L, Nielsen JS, Campos R, Kjems J, Malinowska E, Ferapontova EE. Electroanalysis of pM-levels of urokinase plasminogen activator in serum by phosphorothioated RNA aptamer. Analyst 2016; 140:3794-802. [PMID: 25620243 DOI: 10.1039/c4an02354d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein biomarkers of cancer allow a dramatic improvement in cancer diagnostics as compared to the traditional histological characterisation of tumours by enabling a non-invasive analysis of cancer development and treatment. Here, an electrochemical label-free assay for urokinase plasminogen activator (uPA), a universal biomarker of several cancers, has been developed based on the recently selected uPA-specific fluorinated RNA aptamer, tethered to a gold electrode via a phosphorothioated dA tag, and soluble redox indicators. The binding properties of the uPA-aptamer couple and interference from the non-specific adsorption of bovine serum albumin (BSA) were modulated by the electrode surface charge. A nM uPA electroanalysis at positively charged surfaces, complicated by the competitive adsorption of BSA, was tuned to the pM uPA analysis at negative surface charges of the electrode, being improved in the presence of negatively charged BSA. The aptamer affinity for uPA displayed via the binding/dissociation constant relationship correspondingly increased, ca. three orders of magnitude, from 0.441 to 367. Under optimal conditions, the aptasensor allowed 10(-12)-10(-9) M uPA analysis, also in serum, being practically useful for clinical applications. The proposed strategy for optimization of the electrochemical protein sensing is of particular importance for the assessment and optimization of in vivo protein ligand binding by surface-tethered aptamers.
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Affiliation(s)
- Marta Jarczewska
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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20
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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21
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Cunningham JC, Brenes NJ, Crooks RM. Paper Electrochemical Device for Detection of DNA and Thrombin by Target-Induced Conformational Switching. Anal Chem 2014; 86:6166-70. [DOI: 10.1021/ac501438y] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Josephine C. Cunningham
- Department of Chemistry, The University of Texas at Austin, 105
E. 24th St., Stop A5300, Austin, Texas 78712-1224, United States
| | - Nicholas J. Brenes
- Department of Chemistry, The University of Texas at Austin, 105
E. 24th St., Stop A5300, Austin, Texas 78712-1224, United States
| | - Richard M. Crooks
- Department of Chemistry, The University of Texas at Austin, 105
E. 24th St., Stop A5300, Austin, Texas 78712-1224, United States
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22
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Li Z, Zhang L, Mo H, Peng Y, Zhang H, Xu Z, Zheng C, Lu Z. Size-fitting effect for hybridization of DNA/mercaptohexanol mixed monolayers on gold. Analyst 2014; 139:3137-45. [DOI: 10.1039/c4an00280f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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